SUPERFAMILY 1.75 HMM library and genome assignments server

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Family 10 polysaccharide lyase alignments

These alignments are sequences aligned to the 0038318 model.

Sophisticated options are available for refining alignments:


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Alignments

The numbers along the top are the segment numbers of the HMM states, and each sequence is seperately aligned to the model.
The first sequence is the seed the model was built from.
Upper case letters are aligned, lower case letters are insertions, '-' signifies a deletion and '.' is nothing.

                                                                                      10        20  
                                                                                       |         |  
d1gxma_ .......................................................mtgrmltldgnpaan---------------WLNNART
d1r76a_ avigmneaasaltpsrvsslpdtqraawqeylarseaqlsrdkaslaaelapgqplppppaegkgadtmp------------LDKPAAWYTS


              30        40        50        60                                 70        80         
               |         |         |         |                                  |         |         
d1gxma_ KWSASRADVVLSYQQNNGGWPKNLDYNSVGNGGGGNES.........................GTIDNGATITEMVFLAEVYKSGGNT...K
d1r76a_ KAARHVADVIVSFQTPAGGWGKNQPRDGALRLPGQHYTgenvakvksgsndldaardrdwhyvGTIDNDATVTEIRFLAQVVSQLAPEeaaP


          90       100       110       120       130       140       150       160       170       1
           |         |         |         |         |         |         |         |         |        
d1gxma_ YRDAVRKAANFLVNSQYSTGALPQFYPLKGGYSDHATFNDNGMAYALTVLDFAANKRAPFDTDVFSDNDRTRFKTAVTKGTDYILKAQWKQN
d1r76a_ YRDAALKGIEYLLASQFPNGGWPQVWPLEGGYHDAITYNDDALVHVAELLSDIAAGRDGFG--FVPPAIRTRALEATNAAIHCIVETQVVQD


        80       190       200       210       220        230       240       250       260       27
         |         |         |         |         |          |         |         |         |         
d1gxma_ GVLTVWCAQHGALDYQPKKARAYELESLSGSESVGVLAFLMTQP.QTAEIEQAVRAGVAWFNSPRTYLEGYTYDSSLAATNPIVPRAGSKMW
d1r76a_ GKRLGWGQQHDALTLRPTSARNFEPAALSSTESARILLFLMEIEaPSDAVKQAIRGGVAWLNTSVIRDRAWVKS--DQGYQLVTEQGAKPLW


        0       280       290       300       310       320          
        |         |         |         |         |         |          
d1gxma_ YRFYDLNTNRGFFSDRDGSKFYDITQMSLERRTGYSWGGNYGTSIINFA------qkvgyl
d1r76a_ SRFYSLDGNKPVFGDRDKTIHDDVMGISQERRTGYAWYTTSPQKALSAFTKW---ekrs..


Statistics on alignment.   Save alignment.

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Refine alignments

Sophisticated options are available for refining alignments:

Add your sequences to the alignment:
Members of the same: including
Include all superfamily members: , or just those assigned by the selected model:
Initial T99 seed sequence: NoYes

You may enter many sequences at once using
FASTA format:

Upload a multiple sequence FASTA file:




Model: 0038318 (list models)
Initial SAMT99 seed:
Alignment:



Display Options:
Output in FASTA-like format: NoYes
Output column indices: NoYes
Sequence index (number) on each line: NoYes

Max number of insertions shown: (0 does not show insertions)
Characters per line:
Character to show inserts:
Maximum number of sequences:
Exclude sequences shorter than: residues



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Add alignments from genomes

Select below additional genomes you would like to see alignments for, then click on 'Re-Submit'. The genome assignments will be added to this page.


Select to display   Genome
NoYes   Clostridium cellulolyticum H10
NoYes   Ruminococcus albus 7
NoYes   Clostridium lentocellum DSM 5427
NoYes   Clostridium sp. BNL1100
NoYes   Clostridium cellulovorans 743B
NoYes   Paenibacillus mucilaginosus 3016
NoYes   Paenibacillus polymyxa M1
NoYes   Bacillus clausii KSM-K16
NoYes   Melioribacter roseus P3M
NoYes   Haliscomenobacter hydrossis DSM 1100
NoYes   Niastella koreensis GR20-10
NoYes   Cyclobacterium marinum DSM 745
NoYes   Leadbetterella byssophila DSM 17132
NoYes   Prevotella ruminicola 23
NoYes   Bacteroides salanitronis DSM 18170
NoYes   Bacteroides vulgatus ATCC 8482
NoYes   Bacteroides thetaiotaomicron VPI-5482
NoYes   Pedobacter heparinus DSM 2366
NoYes   Sphingobacterium sp. 21
NoYes   Flavobacteriaceae bacterium 3519-10
NoYes   Flavobacterium branchiophilum FL-15
NoYes   Flavobacterium johnsoniae UW101
NoYes   Fibrobacter succinogenes subsp. succinogenes S85
NoYes   Planctomyces brasiliensis DSM 5305
NoYes   Planctomyces limnophilus DSM 3776
NoYes   Rhodopirellula baltica SH 1
NoYes   Opitutus terrae PB90-1
NoYes   Candidatus Solibacter usitatus Ellin6076
NoYes   Granulicella tundricola MP5ACTX9
NoYes   Granulicella mallensis MP5ACTX8
NoYes   Asticcacaulis excentricus CB 48
NoYes   Brevundimonas subvibrioides ATCC 15264
NoYes   Hirschia baltica ATCC 49814
NoYes   Saccharophagus degradans 2-40
NoYes   Teredinibacter turnerae T7901
NoYes   Cellvibrio japonicus Ueda107
NoYes   Marinomonas mediterranea MMB-1
NoYes   Pseudoxanthomonas suwonensis 11-1
NoYes   Xanthomonas campestris pv. campestris str. B100
NoYes   Dickeya zeae Ech1591
NoYes   Paenibacillus mucilaginosus KNP414
NoYes   Paenibacillus mucilaginosus K02
NoYes   Paenibacillus polymyxa CR1
NoYes   Paenibacillus polymyxa SC2
NoYes   Paenibacillus polymyxa E681
NoYes   Echinicola vietnamensis DSM 17526
NoYes   Bacteroides xylanisolvens XB1A
NoYes   Fibrobacter succinogenes subsp. succinogenes S85
NoYes   Singulisphaera acidiphila DSM 18658
NoYes   Sorangium cellulosum So0157-2
NoYes   Simiduia agarivorans SA1 = DSM 21679
NoYes   Xanthomonas campestris pv. raphani 756C
NoYes   Xanthomonas campestris pv. campestris str. 8004
NoYes   Xanthomonas campestris pv. campestris str. ATCC 33913
NoYes   Air microbial communities Singapore indoor air filters 1 (meta-genome)
NoYes   Air microbial communities Singapore indoor air filters 2 (meta-genome)
NoYes   Combined (meta-genome)
NoYes   Cyphomyrmex longiscapus fungus garden (meta-genome)
NoYes   Dump top (Dump top) (meta-genome)
NoYes   Fungus garden microbial communities from Atta colombica in Panama, sample from fungus garden top (meta-genome)
NoYes   Maize field bulk soil microbial communities from University of Illinois Energy Farm, Urbana, IL (Bulk soil sample from field growing corn (Zea may (meta-genome)
NoYes   Methylotrophic community from Lake Washington sediment combined (v2) (meta-genome)
NoYes   Methylotrophic community from Lake Washington sediment Methane enrichment (meta-genome)
NoYes   Methylotrophic community from Lake Washington sediment Methanol enrichment (meta-genome)
NoYes   Methylotrophic community from Lake Washington sediment Methylamine enrichment (meta-genome)
NoYes   NCBI 2017_08 genome
NoYes   Oak Ridge Pristine Groundwater FRC FW301 (meta-genome)
NoYes   simLC - Simulated Low Complexity Metagenome (meta-genome)
NoYes   Soil microbial communities from sample at FACE Site 1 Maryland Estuary CO2- (Maryland Estuary ambient) (meta-genome)
NoYes   Soil microbial communities from sample at FACE Site 3 Nevada Test Site Creosote CO2+ (meta-genome)
NoYes   Soil microbial communities from sample at FACE Site 3 Nevada Test Site Creosote CO2- (meta-genome)
NoYes   Soil microbial communities from sample at FACE Site 4 Nevada Test Site Crust CO2- (meta-genome)
NoYes   Soil microbial communities from sample at FACE Site 5 Oak Ridge CO2+ (Oak Ridge elevated CO2) (meta-genome)
NoYes   Soil microbial communities from sample at FACE Site 5 Oak Ridge CO2- (Oak Ridge ambient) (meta-genome)
NoYes   STRING v9.0.5 (STRING)
NoYes   Switchgrass rhizosphere microbial community from Michigan, US, sample from East Lansing bulk soil (meta-genome)
NoYes   Uniprot 2018_03 genome
NoYes   Global Ocean Sampling Expedition (GOS)
NoYes   NCBI plasmid sequences (Plasmids)
NoYes   PDB chains (SCOP 1.75) (PDB)
NoYes   Protein Data Bank (all PDB sequenc)
NoYes   SCOP2 SCOPe CATH ECOD (all domain sequ)
NoYes   ALL (only advised for small superfamilies)


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